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PubMed2000

Rapid access to infrared reference spectra of arbitrary organic compounds: scope and limitations of an approach to the simulation of infrared spectra by neural networks

Substance identification by infrared spectroscopy is performed by comparison of the experimental spectrum with a reference spectrum from a printed compilation or a database. If the analyzed compound can not be found in a database the corresponding reference spectrum has to be simulated. In order to achieve this, several reasonable candidates of structures for the compound at hand have to be conceived and for all these, infrared spectra have to be developed. The simulated spectrum that is most similar to the experimental suggests the correct structure. A rapid spectrum prediction method based on neural networks has been developed that supplies reference spectra for any organic compound. The scope and limitations of this method will be discussed on a test set of 16 compounds representing a broad range of organic chemistry.

Journal Article↗
PubMed2000

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/

Animals↗
PubMedDate not supplied

Wheat gliadin: digital imaging and database construction using a 4-band reference system of agarose isoelectric focusing patterns.

An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.

Databases, Factual↗
PubMed1996

Networking consumer health information: bringing the patient into the medical information loop.

The Library of the Health Sciences at the University of Illinois at Chicago obtained a grant from the Illinois State Library to implement a statewide demonstration project that would provide consumer health information (CHI) using InfoTrac's Health Reference Center CD-ROM database. The goals of the project were to cooperate with targeted public libraries and clinics in providing CHI at the earliest point of need; to provide access to the database via a dial-up network server and a toll-free telephone number; and to work with targeted sites on database training, core CHI reference sources, and referral procedures. This paper provides background information about the project; describes the major systems and technical issues encountered; and discusses the outcomes, impact, and envisioned enhancements.

CD-ROM↗
PubMed2002

An expectation maximization algorithm for training hidden substitution models.

We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the Pfam database. Measuring the accuracy of multiple alignment algorithms with reference to BAliBASE (a database of structural reference alignments) our substitution matrices consistently outperform the PAM series, with the improvement steadily increasing as up to four hidden site classes are added. We discuss several applications of this algorithm in bioinformatics.

Algorithms↗
PubMed1999

Comparison of literature searches on quality and costs for health technology assessment using the MEDLINE and EMBASE databases.

Biomedical databases are an important source of information for health technology assessment. However, there is considerable variation in the costs of accessing commercial databases. We sought to measure the quality, amount of overlap, and costs of information retrieved from two of the main database sources--MEDLINE and EMBASE. Librarians at two health technology assessment agencies ran a total of eight literature searches on various medical technologies, using both databases. All search results were independently reviewed by two researchers. The researchers were asked to identify relevant references and to rank each of these according to a level of evidence scale. The results were tabulated to show the number of references identified by each database, the number of relevant references ranked by level of evidence, and the number of these references that were unique to one or the other database. The cost of retrieving references from each source was also calculated. Each database contained relevant references not available in the other. Because of the longer time lag for indexing in MEDLINE, many of the references that originally appeared to be unique to EMBASE were subsequently available in MEDLINE as well. Since our study was conducted, MEDLINE has been made available worldwide, free of charge, via the Internet. Hence, the cost difference between the databases is now even greater. However, notwithstanding the costs, it appears that literature searches that rely on only one or the other database will inevitably miss pertinent information.

Abstracting and Indexing↗
PubMed2003

PGDB: a curated and integrated database of genes related to the prostate.

The Prostate Gene Database (PGDB: http://www.ucsf.edu/pgdb) is a curated and integrated database of genes or genomic loci related to the human prostate and prostatic diseases. Currently, PGDB covers genes involved in a number of molecular and genetic events of the prostate including gene amplification, mutation, gross deletion, methylation, polymorphism, linkage and over-expression, as published in the literature. Genes that are specifically expressed in prostate, as evidenced by analysis of data from expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), are also included. There are a total of 165 unique entries in the database. Users can either browse or query the PGDB through a web interface. For each gene, in addition to basic gene information and rich cross-references to other databases, inclusive and relevant literature references are provided to support the inclusion of the gene in the database. Detailed expression data calculated from the UniGene and SAGEmap databases are also presented.

Databases, Genetic↗
PubMed1999

The Eukaryotic Promoter Database (EPD): recent developments.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Recent efforts have focused on exhaustive cross-referencing to the EMBL nucleotide sequence database, and on the improvement of the WWW-based user interfaces and data retrieval mechanisms. EPD can be accessed at http://www.epd.isb-sib.ch

Algorithms↗
PubMed2026

Performance of MALDI-TOF MS for human Capnocytophaga identification verified by whole-genome sequencing.

OBJECTIVE: This study aims to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification of human Capnocytophaga and to confirm results by whole-genome sequencing. METHODS: Six reference strains, representing human Capnocytophaga species and one taxon, and a total of 126 clinical strains, selected based on their biochemical profiles from a large collection of preliminarily identified Capnocytophaga isolates, were analyzed. RESULTS: Of those, 125 strains (94%) were identified at least at the genus level (log score variation of 1.7-1.999), while 52 strains (39%) were identified at the species level with a cut-off score of &#x2265;2.0. Eight strains (6%) remained unidentified with a log score of <1.69. C. leadbetteri and Capnocytophaga genospecies AHN8471 strains were accurately identified at the genus level. Minor identification errors were observed in three cases: C. leadbetteri (n=1), C. ochracea (n=2), and Capnocytophaga genospecies AHN8471 (n=38). MALDI-TOF MS was unable to distinguish between C. sputigena and Capnocytophaga genospecies AHN8471 at the species level but clustered them together in the Main Spectra Profile (MSP) dendrogram. CONCLUSIONS: MALDI-TOF MS shows promise as a diagnostic tool for identifying human Capnocytophaga species when correct taxonomy and sufficient reference strains are available in the database. Based on the close phenotypic, ribosomal, and genotypic structures, we propose to establish the term "C. sputigena group" encompassing C. sputigena, Capnocytophaga genospecies AHN8471, and other related Capnocytophaga variants. Nevertheless, updating and expanding the MALDI-TOF MS reference database is essential to improve identification accuracy.

Capnocytophaga spp.↗
PubMed1998

The Eukaryotic Promoter Database EPD.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a transcription initiation site. All information presented in EPD results from an independent evaluation of primary experimental data shown in the biological literature. Sequences flanking transcription initiation sites are indirectly given by pointers to EMBL sequences. The annotation part of a promoter entry includes description of the promoter-defining evidence, cross-references to other databases, and bibliographic references. Being designed as a resource for comparative sequence analysis, EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets. The database is available through the World Wide Web at URL http://cmpteam4.unil.ch

Animals↗
PubMed1985

Electronic databases.

Electronic databases corresponding to most of the world's currently published literature and many other types of information are publicly available through online systems. Scientific databases that give references for publications are numerous and widely used; scientific numeric databases that are open to the public are far fewer and less used. Online retrieval systems are becoming easier to use as a result of the introduction of artificial intelligence techniques and user-friendly front ends and gateways. Issues related to electronic databases include public-private sector competition, transborder data flow, copyright, downloading, and the changing roles in database generation and processing.

Bibliographies as Topic↗
PubMed1997

Evaluation of drug interaction document citation in nine on-line bibliographic databases.

OBJECTIVE: To compare nine on-line bibliographic databases to obtain bibliographic references on specific drug interactions. DESIGN: Seven bibliographic databases were selected for their ability to provide information concerning drug interactions: EMBASE, MEDLINE, TOXLINE, BIOSIS, Chemical Abstracts (CAS), PHARMLINE, and International Pharmaceutical Abstracts (IPA). Two French on-line bibliographic databases (i.e., PASCAL, BIBLIOGRAPHIF) were also tested to compare them with the other international databases. Twenty drug interactions were selected randomly using the journal Reactions Weekly 1993. MAIN OUTCOMES MEASURES: The total number of references, the number of potentially relevant references, the number of case report references, the number of unique references in the total number of references, and the number of unique references between potentially relevant references were analyzed by using the Friedman two-way ANOVA by ranks. For each database, relevance and relative recall were calculated. RESULTS: For the total number of references, EMBASE was significantly more comprehensive then all other databases (p < 0.05). EMBASE had a significantly greater number of potentially relevant references than IPA, PHARMLINE, CAS, and BIBLIOGRAPHIF (p < 0.05). For the total number of case report references, only one significant difference, between EMBASE and BIBLIOGRAPHIF (p < 0.05), was observed. MEDLINE and TOXLINE had the lowest cost per potentially relevant reference. CONCLUSIONS: To obtain bibliographic references on drug interactions, the first step should be to search MEDLINE or TOXLINE; the second step, for completeness, should be to search EMBASE.

Databases, Bibliographic↗
PubMed2003

RefDB: a database of uniformly referenced protein chemical shifts.

RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website.

Animals↗
PubMed1998

[A database for thyroid diseases: evaluation with special reference to potential consequences of a nuclear power plant accident].

The concept of a thyroid disease register based on a relational database system with a structured query language (SQL) is reported. More than 5000 examination findings of benign and malignant thyroid disorders have been recorded so far, covering the period from 1986 to 1996. For epidemiological studies these population-based thyroid diseases data can be allocated to a digital data map by means of the five-digit German postal code. When evaluating the data with regard to the function of the thyroid gland as an indicator of preceding nuclear power plant disasters and fallout, we found neither indicators of an increased incidence of thyroid carcinoma as an aftermath of the Chernobyl disaster nor the occurrence of clusters. The data were supplemented by the results of a survey among all Schleswig-Holstein pathologists involved in the diagnosis of thyroid diseases. Data on childhood carcinoma of the thyroid were also provided by the Childhood Tumor Register of the Institute of Pathology, University of Kiel, and by the Childhood Cancer Register of the University of Mainz.

Databases, Factual↗
PubMed2002

'Human' insulin versus animal insulin in people with diabetes mellitus.

BACKGROUND: Human insulin was introduced for the routine treatment of diabetes mellitus in the early 1980s without adequate comparison of efficacy to animal insulin preparations. First reports of altered hypoglycaemia awareness after transfer to human insulin made physicians and especially patients uncertain about potential adverse effects of human insulin. OBJECTIVES: To assess the effects of different insulin species by evaluating their efficacy (in particular glycaemic control) and adverse effects profile (mainly hypoglycaemia). SEARCH STRATEGY: A highly sensitive search for randomised controlled trials combined with key terms for identifying studies on human versus animal insulin was performed using the Cochrane Library (issue 2, 2002), Medline (1966 to May, 2002) and Embase (1974 to February, 2002). We also searched reference lists and databases of ongoing trials. Date of latest search: May 2002. SELECTION CRITERIA: We included randomised controlled clinical trials with diabetic patients of all ages that compared human to animal (for the most part purified porcine) insulin. Trial duration had to be at least one month in order to achieve reliable results on the main outcome parameter glycated haemoglobin. DATA COLLECTION AND ANALYSIS: Trial selection as well as evaluation of study quality was performed by two independent reviewers. The quality of reporting of each trial was assessed according to a modification of the quality criteria as specified by Schulz and by Jadad. MAIN RESULTS: Altogether 2156 participants took part in the 45 randomised controlled studies that were discovered through extensive search efforts. Though many studies were of a randomised, double-blind design, most studies were of poor methodological quality. Purified porcine and semi-synthetic insulin were most often investigated. No significant differences in metabolic control or hypoglycaemic episodes between various insulin species could be elucidated. Insulin dose and insulin antibodies did not show relevant dissimilarities. REVIEWER'S CONCLUSIONS: A comparison of the effects of human and animal insulin as well as of the adverse reaction profile did not show clinically relevant differences. Many patient-oriented outcomes like health-related quality of life or diabetes complications and mortality were never investigated in high-quality randomised clinical trials. The story of the introduction of human might be repeated by contemporary launching campaigns to introduce pharmaceutical and technological innovations that are not backed up by sufficient proof of their advantages and safety.

Animals↗
PubMed1996

Searching for information on toxicological data of chemical substances in selected bibliographic databases--selection of essential databases for toxicological researches.

By using information from printed and online database guides, 18 online bibliographic databases (BD), which cover literature on toxicology were selected from 5 hosts. A search for literature containing information on three selected chemicals was carried out with each of the databases, and the number of documents relevant to toxicology found in them was compared by computer-assisted analysis. Some databases yielded very little information pertinent to toxicology, while others provided a considerable amount. In addition, the databases contained numerous duplicates (references common to more than one database). Most of the relevant documents could be obtained using only 8 of the 18 BDs selected. These databases are: Biosis Previews (BIOSIS), Chemical Abstracts (CA), Chemical Safety Newsbase (CSNB), Excerpta Medica (EMBASE), National Institute for Occupational Safety and Health (NIOSH), Scisearch, Toxicology Information Online (TOXLINE) and the former Toxicology Literature (TOXLIT).

Databases, Bibliographic↗
PubMed2000

The RESID database of protein structure modifications: 2000 update.

The RESID Database contains supplemental information on post-translational modifications for the standardized annotations appearing in the PIR-International Protein Sequence Database. The RESID Database includes: systematic and frequently observed alternate names, Chemical s Service registry numbers, atomic formulas and weights, enzyme activities, indicators for N-terminal, C-terminal or peptide chain cross-link modifications, keywords, literature citations with database cross-references, structural diagrams and molecular models. Since 1995 updates of the RESID Database have appeared as often as weekly, and full releases appear quarterly. The database is freely accessible through the PIR Web site http://pir.georgetown.edu/pirwww/dbinfo/resid.html and by FTP.

Databases, Factual↗